Casal2 Test Case MPD comparisons for SBW

1 SBW comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-8 vs. 2e-6).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-8 vs. 2e-6). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 SBW model characteristics

The main characteristics of the Test Case SBW (southern blue whiting) CASAL model are:

• one stock, ages 2 - 15
• two areas, spawn and nospawn
• years 1960 - 2015, projection years 2016 - 2021
• two time steps
• two stock categories, male and female
• sex-specific migration from 'nospawn' to 'spawn'
• male and female natural mortality (M) average of 0.2, difference of 0.02
• Beverton-Holt stock-recruitment relationship, with steepness (h) 0.9 and \(\sigma_R\) 1.0
• length-weight relationship (\(W = aL^b\))
• no ageing error
• one fishery in area 'spawn'

Observation data include:

• empirical sex-specific length-at-age data for 1979 - 2015
• survey indices for immature and mature partitions
• fishery sex-specific proportions-at-age

Parameters estimated include:

• B0
• process error for the mature survey index
• the average of and difference between male and female natural mortality
• sex-specific migration rates
• YCS (recruitment deviations)

1.2 R environment

## [1] "Mon Aug  3 12:07:37 2020"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
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## locale:
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##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] casal2_1.0     casal_2.30     devtools_2.3.1 usethis_1.6.1  rlist_0.4.6.1 
##  [6] ggthemes_4.2.0 gridExtra_2.3  coda_0.19-3    ggmcmc_1.4.1   ggplot2_3.3.2 
## [11] tidyr_1.1.0    dplyr_1.0.1   
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.0   xfun_0.16          remotes_2.2.0      purrr_0.3.4       
##  [5] lattice_0.20-38    testthat_2.3.2     colorspace_1.4-1   vctrs_0.3.2       
##  [9] generics_0.0.2     htmltools_0.5.0    yaml_2.2.1         rlang_0.4.7       
## [13] pkgbuild_1.1.0     pillar_1.4.6       glue_1.4.1         withr_2.2.0       
## [17] RColorBrewer_1.1-2 sessioninfo_1.1.1  lifecycle_0.2.0    plyr_1.8.6        
## [21] stringr_1.4.0      munsell_0.5.0      gtable_0.3.0       evaluate_0.14     
## [25] memoise_1.1.0      knitr_1.29         GGally_1.4.0       callr_3.4.3       
## [29] ps_1.3.3           fansi_0.4.1        Rcpp_1.0.5         scales_1.1.1      
## [33] backports_1.1.8    desc_1.2.0         pkgload_1.1.0      fs_1.5.0          
## [37] digest_0.6.25      stringi_1.4.6      processx_3.4.3     grid_3.6.0        
## [41] rprojroot_1.3-2    cli_2.0.2          tools_3.6.0        magrittr_1.5      
## [45] tibble_3.0.3       crayon_1.3.4       pkgconfig_2.0.3    ellipsis_0.3.1    
## [49] data.table_1.13.0  prettyunits_1.1.1  assertthat_0.2.1   rmarkdown_2.3     
## [53] reshape_0.8.8      R6_2.4.1           compiler_3.6.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')

source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates

rownames	Base_Model	Sensitivity_1	Percent_Diff
initialization.B0	314500.00000	314500.00000	0.000
relative_abundance[TangaroaAcousticMature].cv_process_error	0.00010	0.00010	0.000
natural_mortality.avg	0.15580	0.15580	0.000
natural_mortality.diff	-0.00914	-0.00914	0.000
migration[toSpawn].rates_male1	0.08558	0.08558	0.000
migration[toSpawn].rates_male2	0.72990	0.72990	0.000
migration[toSpawn].rates_male3	0.51270	0.51270	0.000
migration[toSpawn].rates_male4	0.33120	0.33120	0.000
migration[toSpawn].rates_male5	0.99000	0.99000	0.000
migration[toSpawn].rates_female1	0.01907	0.01907	0.000
migration[toSpawn].rates_female2	0.51250	0.51250	0.000
migration[toSpawn].rates_female3	0.94120	0.94120	0.000
migration[toSpawn].rates_female4	0.99900	0.99900	0.000
migration[toSpawn].rates_female5	0.99000	0.99000	0.000
recruitment.YCS1	0.25590	0.25590	0.000
recruitment.YCS2	0.26100	0.26100	0.000
recruitment.YCS3	0.26700	0.26700	0.000
recruitment.YCS4	0.27430	0.27430	0.000
recruitment.YCS5	0.28320	0.28320	0.000
recruitment.YCS6	0.29410	0.29410	0.000
recruitment.YCS7	0.30880	0.30880	0.000
recruitment.YCS8	0.82470	0.82470	0.000
recruitment.YCS9	0.53160	0.53160	0.000
recruitment.YCS10	0.37070	0.37070	0.000
recruitment.YCS11	0.26680	0.26680	0.000
recruitment.YCS12	0.13850	0.13850	0.000
recruitment.YCS13	0.08025	0.08025	0.000
recruitment.YCS14	0.15820	0.15820	0.000
recruitment.YCS15	0.10630	0.10630	0.000
recruitment.YCS16	0.05757	0.05757	0.000
recruitment.YCS17	0.06079	0.06079	0.000
recruitment.YCS18	0.12720	0.12720	0.000
recruitment.YCS19	0.05057	0.05057	0.000
recruitment.YCS20	0.03959	0.03959	0.000
recruitment.YCS21	0.04996	0.04996	0.000
recruitment.YCS22	0.37590	0.37590	0.000
recruitment.YCS23	0.36820	0.36820	0.000
recruitment.YCS24	0.09402	0.09402	0.000
recruitment.YCS25	0.03280	0.03280	0.000
recruitment.YCS26	0.13650	0.13650	0.000
recruitment.YCS27	0.13080	0.13080	0.000
recruitment.YCS28	0.11260	0.11260	0.000
recruitment.YCS29	0.28620	0.28620	0.000
recruitment.YCS30	0.12790	0.12790	0.000
recruitment.YCS31	0.43770	0.43770	0.000
recruitment.YCS32	0.03590	0.03590	0.000
recruitment.YCS33	0.25650	0.25650	0.000
recruitment.YCS34	2.75100	2.75100	0.000
recruitment.YCS35	0.55870	0.55870	0.000
recruitment.YCS36	0.26390	0.26390	0.000
recruitment.YCS37	0.12670	0.12670	0.000
recruitment.YCS38	0.56000	0.56000	0.000
recruitment.YCS39	0.36190	0.36190	0.000
recruitment.YCS40	0.14490	0.14490	0.000
recruitment.YCS41	0.32060	0.32060	0.000
recruitment.YCS42	0.19280	0.19280	0.000
recruitment.YCS43	0.29870	0.29870	0.000
recruitment.YCS44	0.70520	0.70520	0.000
recruitment.YCS45	0.41770	0.41770	0.000
recruitment.YCS46	0.25430	0.25430	0.000
recruitment.YCS47	0.25240	0.25240	0.000
recruitment.YCS48	0.32500	0.32500	0.000
recruitment.YCS49	1.69600	1.69600	0.000
recruitment.YCS50	0.68660	0.68660	0.000
recruitment.YCS51	0.20070	0.20070	0.000
recruitment.YCS52	1.20400	1.20400	0.000
recruitment.YCS53	0.16930	0.16930	0.000
recruitment.YCS54	0.87570	0.87570	0.000
recruitment.YCS55	0.13270	0.13270	0.000
recruitment.YCS56	1.00000	1.00000	0.000

Casal2 parameter estimates

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	299610.00000	298978.00000	299610.00000	314527.00000	314527.00000	299610.00000	299610.00000	299610.00000
selectivity[MaturationSel_male].v{1}	0.08537	0.08529	0.08537	0.08558	0.08558	0.08537	0.08537	0.08537
selectivity[MaturationSel_male].v{2}	0.73526	0.73346	0.73526	0.72993	0.72993	0.73526	0.73526	0.73526
selectivity[MaturationSel_male].v{3}	0.51432	0.58196	0.51432	0.51267	0.51267	0.51432	0.51432	0.51432
selectivity[MaturationSel_male].v{4}	0.29398	0.00100	0.29398	0.33118	0.33118	0.29398	0.29398	0.29398
selectivity[MaturationSel_female].v{1}	0.01903	0.01901	0.01903	0.01907	0.01907	0.01903	0.01903	0.01903
selectivity[MaturationSel_female].v{2}	0.51564	0.51406	0.51564	0.51254	0.51254	0.51564	0.51564	0.51564
selectivity[MaturationSel_female].v{3}	0.94578	0.93978	0.94578	0.94120	0.94120	0.94578	0.94578	0.94578
selectivity[MaturationSel_female].v{4}	0.99900	0.99900	0.99900	0.99900	0.99900	0.99900	0.99900	0.99900
process[Recruitment].ycs_values{1958}	0.25169	0.25201	0.25169	0.25590	0.25590	0.25169	0.25169	0.25169
process[Recruitment].ycs_values{1959}	0.25626	0.25668	0.25626	0.26099	0.26099	0.25626	0.25626	0.25626
process[Recruitment].ycs_values{1960}	0.26170	0.26222	0.26170	0.26702	0.26702	0.26170	0.26170	0.26170
process[Recruitment].ycs_values{1961}	0.26830	0.26898	0.26830	0.27431	0.27431	0.26830	0.26830	0.26830
process[Recruitment].ycs_values{1962}	0.27632	0.27722	0.27632	0.28317	0.28317	0.27632	0.27632	0.27632
process[Recruitment].ycs_values{1963}	0.28636	0.28756	0.28636	0.29410	0.29410	0.28636	0.28636	0.28636
process[Recruitment].ycs_values{1964}	0.30009	0.30176	0.30009	0.30880	0.30880	0.30009	0.30009	0.30009
process[Recruitment].ycs_values{1965}	0.70701	0.71254	0.70701	0.82468	0.82468	0.70701	0.70701	0.70701
process[Recruitment].ycs_values{1966}	0.46402	0.46571	0.46402	0.53162	0.53162	0.46402	0.46402	0.46402
process[Recruitment].ycs_values{1967}	0.32237	0.32309	0.32237	0.37070	0.37070	0.32237	0.32237	0.32237
process[Recruitment].ycs_values{1968}	0.23172	0.23203	0.23172	0.26676	0.26676	0.23172	0.23172	0.23172
process[Recruitment].ycs_values{1969}	0.12143	0.12156	0.12143	0.13853	0.13853	0.12143	0.12143	0.12143
process[Recruitment].ycs_values{1970}	0.07084	0.07096	0.07084	0.08025	0.08025	0.07084	0.07084	0.07084
process[Recruitment].ycs_values{1971}	0.13612	0.13621	0.13612	0.15822	0.15822	0.13612	0.13612	0.13612
process[Recruitment].ycs_values{1972}	0.09151	0.09154	0.09151	0.10630	0.10630	0.09151	0.09151	0.09151
process[Recruitment].ycs_values{1973}	0.04983	0.04988	0.04983	0.05757	0.05757	0.04983	0.04983	0.04983
process[Recruitment].ycs_values{1974}	0.05215	0.05210	0.05215	0.06079	0.06079	0.05215	0.05215	0.05215
process[Recruitment].ycs_values{1975}	0.10750	0.10762	0.10750	0.12725	0.12725	0.10750	0.10750	0.10750
process[Recruitment].ycs_values{1976}	0.04308	0.04319	0.04308	0.05057	0.05057	0.04308	0.04308	0.04308
process[Recruitment].ycs_values{1977}	0.03373	0.03372	0.03373	0.03959	0.03959	0.03373	0.03373	0.03373
process[Recruitment].ycs_values{1978}	0.04227	0.04226	0.04227	0.04996	0.04996	0.04227	0.04227	0.04227
process[Recruitment].ycs_values{1979}	0.31277	0.31305	0.31277	0.37587	0.37587	0.31277	0.31277	0.31277
process[Recruitment].ycs_values{1980}	0.30480	0.30473	0.30480	0.36816	0.36816	0.30480	0.30480	0.30480
process[Recruitment].ycs_values{1981}	0.07799	0.07795	0.07799	0.09402	0.09402	0.07799	0.07799	0.07799
process[Recruitment].ycs_values{1982}	0.02751	0.02752	0.02751	0.03280	0.03280	0.02751	0.02751	0.02751
process[Recruitment].ycs_values{1983}	0.11248	0.11236	0.11248	0.13647	0.13647	0.11248	0.11248	0.11248
process[Recruitment].ycs_values{1984}	0.10757	0.10735	0.10757	0.13081	0.13081	0.10757	0.10757	0.10757
process[Recruitment].ycs_values{1985}	0.09256	0.09261	0.09256	0.11256	0.11256	0.09256	0.09256	0.09256
process[Recruitment].ycs_values{1986}	0.23474	0.23557	0.23474	0.28616	0.28616	0.23474	0.23474	0.23474
process[Recruitment].ycs_values{1987}	0.10518	0.10504	0.10518	0.12793	0.12793	0.10518	0.10518	0.10518
process[Recruitment].ycs_values{1988}	0.35849	0.35860	0.35849	0.43772	0.43772	0.35849	0.35849	0.35849
process[Recruitment].ycs_values{1989}	0.03001	0.03004	0.03001	0.03590	0.03590	0.03001	0.03001	0.03001
process[Recruitment].ycs_values{1990}	0.21160	0.21190	0.21160	0.25649	0.25649	0.21160	0.21160	0.21160
process[Recruitment].ycs_values{1991}	2.26862	2.26986	2.26862	2.75116	2.75116	2.26862	2.26862	2.26862
process[Recruitment].ycs_values{1992}	0.46042	0.46088	0.46042	0.55871	0.55871	0.46042	0.46042	0.46042
process[Recruitment].ycs_values{1993}	0.21818	0.21922	0.21818	0.26390	0.26390	0.21818	0.21818	0.21818
process[Recruitment].ycs_values{1994}	0.10632	0.10635	0.10632	0.12675	0.12675	0.10632	0.10632	0.10632
process[Recruitment].ycs_values{1995}	0.46220	0.45825	0.46220	0.56002	0.56002	0.46220	0.46220	0.46220
process[Recruitment].ycs_values{1996}	0.29958	0.30149	0.29958	0.36192	0.36192	0.29958	0.29958	0.29958
process[Recruitment].ycs_values{1997}	0.12096	0.12048	0.12096	0.14486	0.14486	0.12096	0.12096	0.12096
process[Recruitment].ycs_values{1998}	0.26476	0.26596	0.26476	0.32060	0.32060	0.26476	0.26476	0.26476
process[Recruitment].ycs_values{1999}	0.16048	0.15944	0.16048	0.19279	0.19279	0.16048	0.16048	0.16048
process[Recruitment].ycs_values{2000}	0.24624	0.24727	0.24624	0.29874	0.29874	0.24624	0.24624	0.24624
process[Recruitment].ycs_values{2001}	0.57498	0.57294	0.57498	0.70518	0.70518	0.57498	0.57498	0.57498
process[Recruitment].ycs_values{2002}	0.33816	0.33919	0.33816	0.41769	0.41769	0.33816	0.33816	0.33816
process[Recruitment].ycs_values{2003}	0.20585	0.20534	0.20585	0.25427	0.25427	0.20585	0.20585	0.20585
process[Recruitment].ycs_values{2004}	0.20174	0.20091	0.20174	0.25238	0.25238	0.20174	0.20174	0.20174
process[Recruitment].ycs_values{2005}	0.25678	0.25655	0.25678	0.32495	0.32495	0.25678	0.25678	0.25678
process[Recruitment].ycs_values{2006}	1.31409	1.31392	1.31409	1.69567	1.69567	1.31409	1.31409	1.31409
process[Recruitment].ycs_values{2007}	0.52328	0.52067	0.52328	0.68660	0.68660	0.52328	0.52328	0.52328
process[Recruitment].ycs_values{2008}	0.15242	0.15133	0.15242	0.20067	0.20067	0.15242	0.15242	0.15242
process[Recruitment].ycs_values{2009}	0.87606	0.86701	0.87606	1.20372	1.20372	0.87606	0.87606	0.87606
process[Recruitment].ycs_values{2010}	0.00772	0.00772	0.00772	0.16935	0.16935	0.00772	0.00772	0.00772
process[Recruitment].ycs_values{2011}	0.59070	0.58506	0.59070	0.87569	0.87569	0.59070	0.59070	0.59070
process[Recruitment].ycs_values{2012}	0.09495	0.09453	0.09495	0.13266	0.13266	0.09495	0.09495	0.09495
process[Instantaneous_Mortality].m{male.nonspawn}	0.15745	0.15777	0.15745	0.15118	0.15118	0.15745	0.15745	0.15745
process[Instantaneous_Mortality].m{female.nonspawn}	0.16651	0.16689	0.16651	0.16033	0.16033	0.16651	0.16651	0.16651
observation[TangaroaAcousticMature].process_error	0.00010	0.00010	0.00010	0.00010	0.00010	0.00010	0.00010	0.00010

Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
process[Recruitment].b0	0.000	0.211	0.000	-4.979	-4.979	0.000	0.000	0.000
selectivity[MaturationSel_male].v{1}	0.000	0.085	0.000	-0.254	-0.254	0.000	0.000	0.000
selectivity[MaturationSel_male].v{2}	0.000	0.244	0.000	0.725	0.725	0.000	0.000	0.000
selectivity[MaturationSel_male].v{3}	0.000	-13.150	0.000	0.321	0.321	0.000	0.000	0.000
selectivity[MaturationSel_male].v{4}	0.000	99.660	0.000	-12.654	-12.654	0.000	0.000	0.000
selectivity[MaturationSel_female].v{1}	0.000	0.125	0.000	-0.211	-0.211	0.000	0.000	0.000
selectivity[MaturationSel_female].v{2}	0.000	0.305	0.000	0.601	0.601	0.000	0.000	0.000
selectivity[MaturationSel_female].v{3}	0.000	0.635	0.000	0.484	0.484	0.000	0.000	0.000
selectivity[MaturationSel_female].v{4}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
process[Recruitment].ycs_values{1958}	0.000	-0.130	0.000	-1.673	-1.673	0.000	0.000	0.000
process[Recruitment].ycs_values{1959}	0.000	-0.161	0.000	-1.847	-1.847	0.000	0.000	0.000
process[Recruitment].ycs_values{1960}	0.000	-0.200	0.000	-2.036	-2.036	0.000	0.000	0.000
process[Recruitment].ycs_values{1961}	0.000	-0.255	0.000	-2.243	-2.243	0.000	0.000	0.000
process[Recruitment].ycs_values{1962}	0.000	-0.325	0.000	-2.479	-2.479	0.000	0.000	0.000
process[Recruitment].ycs_values{1963}	0.000	-0.420	0.000	-2.703	-2.703	0.000	0.000	0.000
process[Recruitment].ycs_values{1964}	0.000	-0.559	0.000	-2.902	-2.902	0.000	0.000	0.000
process[Recruitment].ycs_values{1965}	0.000	-0.782	0.000	-16.643	-16.643	0.000	0.000	0.000
process[Recruitment].ycs_values{1966}	0.000	-0.364	0.000	-14.570	-14.570	0.000	0.000	0.000
process[Recruitment].ycs_values{1967}	0.000	-0.224	0.000	-14.993	-14.993	0.000	0.000	0.000
process[Recruitment].ycs_values{1968}	0.000	-0.132	0.000	-15.121	-15.121	0.000	0.000	0.000
process[Recruitment].ycs_values{1969}	0.000	-0.107	0.000	-14.081	-14.081	0.000	0.000	0.000
process[Recruitment].ycs_values{1970}	0.000	-0.181	0.000	-13.297	-13.297	0.000	0.000	0.000
process[Recruitment].ycs_values{1971}	0.000	-0.064	0.000	-16.229	-16.229	0.000	0.000	0.000
process[Recruitment].ycs_values{1972}	0.000	-0.038	0.000	-16.169	-16.169	0.000	0.000	0.000
process[Recruitment].ycs_values{1973}	0.000	-0.098	0.000	-15.536	-15.536	0.000	0.000	0.000
process[Recruitment].ycs_values{1974}	0.000	0.098	0.000	-16.571	-16.571	0.000	0.000	0.000
process[Recruitment].ycs_values{1975}	0.000	-0.105	0.000	-18.367	-18.367	0.000	0.000	0.000
process[Recruitment].ycs_values{1976}	0.000	-0.260	0.000	-17.388	-17.388	0.000	0.000	0.000
process[Recruitment].ycs_values{1977}	0.000	0.025	0.000	-17.382	-17.382	0.000	0.000	0.000
process[Recruitment].ycs_values{1978}	0.000	0.024	0.000	-18.215	-18.215	0.000	0.000	0.000
process[Recruitment].ycs_values{1979}	0.000	-0.090	0.000	-20.174	-20.174	0.000	0.000	0.000
process[Recruitment].ycs_values{1980}	0.000	0.022	0.000	-20.787	-20.787	0.000	0.000	0.000
process[Recruitment].ycs_values{1981}	0.000	0.052	0.000	-20.557	-20.557	0.000	0.000	0.000
process[Recruitment].ycs_values{1982}	0.000	-0.040	0.000	-19.235	-19.235	0.000	0.000	0.000
process[Recruitment].ycs_values{1983}	0.000	0.104	0.000	-21.336	-21.336	0.000	0.000	0.000
process[Recruitment].ycs_values{1984}	0.000	0.205	0.000	-21.602	-21.602	0.000	0.000	0.000
process[Recruitment].ycs_values{1985}	0.000	-0.062	0.000	-21.613	-21.613	0.000	0.000	0.000
process[Recruitment].ycs_values{1986}	0.000	-0.354	0.000	-21.907	-21.907	0.000	0.000	0.000
process[Recruitment].ycs_values{1987}	0.000	0.136	0.000	-21.632	-21.632	0.000	0.000	0.000
process[Recruitment].ycs_values{1988}	0.000	-0.032	0.000	-22.100	-22.100	0.000	0.000	0.000
process[Recruitment].ycs_values{1989}	0.000	-0.121	0.000	-19.633	-19.633	0.000	0.000	0.000
process[Recruitment].ycs_values{1990}	0.000	-0.142	0.000	-21.217	-21.217	0.000	0.000	0.000
process[Recruitment].ycs_values{1991}	0.000	-0.055	0.000	-21.270	-21.270	0.000	0.000	0.000
process[Recruitment].ycs_values{1992}	0.000	-0.101	0.000	-21.350	-21.350	0.000	0.000	0.000
process[Recruitment].ycs_values{1993}	0.000	-0.475	0.000	-20.955	-20.955	0.000	0.000	0.000
process[Recruitment].ycs_values{1994}	0.000	-0.024	0.000	-19.208	-19.208	0.000	0.000	0.000
process[Recruitment].ycs_values{1995}	0.000	0.856	0.000	-21.162	-21.162	0.000	0.000	0.000
process[Recruitment].ycs_values{1996}	0.000	-0.639	0.000	-20.809	-20.809	0.000	0.000	0.000
process[Recruitment].ycs_values{1997}	0.000	0.396	0.000	-19.754	-19.754	0.000	0.000	0.000
process[Recruitment].ycs_values{1998}	0.000	-0.452	0.000	-21.087	-21.087	0.000	0.000	0.000
process[Recruitment].ycs_values{1999}	0.000	0.649	0.000	-20.132	-20.132	0.000	0.000	0.000
process[Recruitment].ycs_values{2000}	0.000	-0.419	0.000	-21.324	-21.324	0.000	0.000	0.000
process[Recruitment].ycs_values{2001}	0.000	0.354	0.000	-22.645	-22.645	0.000	0.000	0.000
process[Recruitment].ycs_values{2002}	0.000	-0.305	0.000	-23.517	-23.517	0.000	0.000	0.000
process[Recruitment].ycs_values{2003}	0.000	0.247	0.000	-23.521	-23.521	0.000	0.000	0.000
process[Recruitment].ycs_values{2004}	0.000	0.415	0.000	-25.098	-25.098	0.000	0.000	0.000
process[Recruitment].ycs_values{2005}	0.000	0.090	0.000	-26.551	-26.551	0.000	0.000	0.000
process[Recruitment].ycs_values{2006}	0.000	0.013	0.000	-29.038	-29.038	0.000	0.000	0.000
process[Recruitment].ycs_values{2007}	0.000	0.500	0.000	-31.210	-31.210	0.000	0.000	0.000
process[Recruitment].ycs_values{2008}	0.000	0.716	0.000	-31.658	-31.658	0.000	0.000	0.000
process[Recruitment].ycs_values{2009}	0.000	1.033	0.000	-37.401	-37.401	0.000	0.000	0.000
process[Recruitment].ycs_values{2010}	0.000	0.026	0.000	-2093.890	-2093.890	0.000	0.000	0.000
process[Recruitment].ycs_values{2011}	0.000	0.955	0.000	-48.246	-48.246	0.000	0.000	0.000
process[Recruitment].ycs_values{2012}	0.000	0.440	0.000	-39.718	-39.718	0.000	0.000	0.000
process[Instantaneous_Mortality].m{male.nonspawn}	0.000	-0.206	0.000	3.978	3.978	0.000	0.000	0.000
process[Instantaneous_Mortality].m{female.nonspawn}	0.000	-0.227	0.000	3.713	3.713	0.000	0.000	0.000
observation[TangaroaAcousticMature].process_error	0.000	0.000	0.000	0.010	0.010	0.000	0.000	0.000

CASAL objective function component values

Component	Base_Model	Sensitivity_1
TangaroaAcousticImmature	17.980	17.980
TangaroaAcousticMature	-9.196	-9.196
ObserverProportionsAtAge	957.800	957.800
prior_on_initialization.B0	12.660	12.660
prior_on_relative_abundance[TangaroaAcousticMature].cv_process_error	-9.210	-9.210
prior_on_natural_mortality.avg	-1.183	-1.183
prior_on_natural_mortality.diff	0.017	0.017
prior_on_migration[toSpawn].rates_male	0.000	0.000
prior_on_migration[toSpawn].rates_female	0.000	0.000
prior_on_recruitment.YCS	-30.170	-30.170
prior_on_q_TangaroaImmatureq	0.000	0.000
prior_on_q_TangaroaMatureq	-0.732	-0.732
Penalty-CatchLimitTrawl	0.000	0.000
Penalty-YCS	0.397	0.397
Total	938.400	938.400

Casal2 objective function component values

rownames	betadiff_casal_flags_on	betadiff_casal_flags_off	betadiff_casal_flags_on_low_tol	cppad_casal_flags_on	cppad_casal_flags_off	adolc_casal_flags_on	adolc_casal_flags_off	adolc_casal_flags_on_low_tol
observation->TangaroaAcousticMature-1993	-1.281	-1.288	-1.281	-1.371	-1.371	-1.281	-1.281	-1.281
observation->TangaroaAcousticMature-1994	-0.601	-0.610	-0.601	-0.439	-0.439	-0.601	-0.601	-0.601
observation->TangaroaAcousticMature-1995	-0.448	-0.416	-0.448	-0.622	-0.622	-0.448	-0.448	-0.448
observation->TangaroaAcousticMature-1998	-1.707	-1.716	-1.707	-1.531	-1.531	-1.707	-1.707	-1.707
observation->TangaroaAcousticMature-2000	-1.778	-1.778	-1.778	-1.764	-1.764	-1.778	-1.778	-1.778
observation->TangaroaAcousticMature-2002	-0.369	-0.371	-0.369	-0.358	-0.358	-0.369	-0.369	-0.369
observation->TangaroaAcousticMature-2004	-0.784	-0.782	-0.784	-0.807	-0.807	-0.784	-0.784	-0.784
observation->TangaroaAcousticMature-2006	-0.888	-0.891	-0.888	-0.881	-0.881	-0.888	-0.888	-0.888
observation->TangaroaAcousticMature-2009	0.699	0.703	0.699	0.455	0.455	0.699	0.699	0.699
observation->TangaroaAcousticMature-2011	-1.004	-1.028	-1.004	-0.638	-0.638	-1.004	-1.004	-1.004
observation->TangaroaAcousticMature-2013	-1.401	-1.401	-1.401	-1.239	-1.239	-1.401	-1.401	-1.401
observation->TangaroaAcousticImmature-1993	1.968	1.958	1.968	2.542	2.542	1.968	1.968	1.968
observation->TangaroaAcousticImmature-1994	0.817	0.800	0.817	0.618	0.618	0.817	0.817	0.817
observation->TangaroaAcousticImmature-1995	1.945	2.247	1.945	2.199	2.199	1.945	1.945	1.945
observation->TangaroaAcousticImmature-1998	-1.536	-1.534	-1.536	-1.444	-1.444	-1.536	-1.536	-1.536
observation->TangaroaAcousticImmature-2000	4.866	5.060	4.866	4.306	4.306	4.866	4.866	4.866
observation->TangaroaAcousticImmature-2002	7.321	7.280	7.321	7.122	7.122	7.321	7.321	7.321
observation->TangaroaAcousticImmature-2004	1.722	1.650	1.722	1.430	1.430	1.722	1.722	1.722
observation->TangaroaAcousticImmature-2006	-0.467	-0.377	-0.467	-0.524	-0.524	-0.467	-0.467	-0.467
observation->TangaroaAcousticImmature-2009	2.221	2.272	2.221	1.845	1.845	2.221	2.221	2.221
observation->TangaroaAcousticImmature-2011	1.543	1.409	1.543	0.514	0.514	1.543	1.543	1.543
observation->TangaroaAcousticImmature-2013	-0.388	-0.346	-0.388	-0.628	-0.628	-0.388	-0.388	-0.388
observation->ObserverProportionsAtAge-1979	15.198	15.184	15.198	15.170	15.170	15.198	15.198	15.198
observation->ObserverProportionsAtAge-1980	17.076	17.066	17.076	16.997	16.997	17.076	17.076	17.076
observation->ObserverProportionsAtAge-1981	30.961	30.956	30.961	30.816	30.816	30.961	30.961	30.961
observation->ObserverProportionsAtAge-1982	26.030	26.014	26.030	25.988	25.988	26.030	26.030	26.030
observation->ObserverProportionsAtAge-1983	20.423	20.414	20.423	20.405	20.405	20.423	20.423	20.423
observation->ObserverProportionsAtAge-1984	26.174	26.253	26.174	26.188	26.188	26.174	26.174	26.174
observation->ObserverProportionsAtAge-1985	22.917	22.931	22.917	22.925	22.925	22.917	22.917	22.917
observation->ObserverProportionsAtAge-1986	27.628	27.619	27.628	27.666	27.666	27.628	27.628	27.628
observation->ObserverProportionsAtAge-1987	28.825	28.824	28.825	28.852	28.852	28.825	28.825	28.825
observation->ObserverProportionsAtAge-1988	28.862	28.865	28.862	28.852	28.852	28.862	28.862	28.862
observation->ObserverProportionsAtAge-1989	31.713	31.724	31.713	31.664	31.664	31.713	31.713	31.713
observation->ObserverProportionsAtAge-1990	28.187	28.096	28.187	28.167	28.167	28.187	28.187	28.187
observation->ObserverProportionsAtAge-1991	37.659	37.513	37.659	37.701	37.701	37.659	37.659	37.659
observation->ObserverProportionsAtAge-1992	28.026	28.087	28.026	28.005	28.005	28.026	28.026	28.026
observation->ObserverProportionsAtAge-1993	29.232	29.287	29.232	29.218	29.218	29.232	29.232	29.232
observation->ObserverProportionsAtAge-1994	22.142	22.164	22.142	22.182	22.182	22.142	22.142	22.142
observation->ObserverProportionsAtAge-1995	21.909	22.002	21.909	21.880	21.880	21.909	21.909	21.909
observation->ObserverProportionsAtAge-1996	25.898	25.676	25.898	25.957	25.957	25.898	25.898	25.898
observation->ObserverProportionsAtAge-1997	21.104	21.130	21.104	21.121	21.121	21.104	21.104	21.104
observation->ObserverProportionsAtAge-1998	20.384	20.350	20.384	20.366	20.366	20.384	20.384	20.384
observation->ObserverProportionsAtAge-1999	24.422	24.427	24.422	24.462	24.462	24.422	24.422	24.422
observation->ObserverProportionsAtAge-2000	16.719	16.742	16.719	16.759	16.759	16.719	16.719	16.719
observation->ObserverProportionsAtAge-2001	26.268	26.258	26.268	26.422	26.422	26.268	26.268	26.268
observation->ObserverProportionsAtAge-2002	20.049	19.992	20.049	20.058	20.058	20.049	20.049	20.049
observation->ObserverProportionsAtAge-2003	34.053	34.120	34.053	33.941	33.941	34.053	34.053	34.053
observation->ObserverProportionsAtAge-2004	18.376	18.403	18.376	18.369	18.369	18.376	18.376	18.376
observation->ObserverProportionsAtAge-2005	27.993	28.002	27.993	28.123	28.123	27.993	27.993	27.993
observation->ObserverProportionsAtAge-2006	23.330	23.323	23.330	23.299	23.299	23.330	23.330	23.330
observation->ObserverProportionsAtAge-2007	26.652	26.679	26.652	26.685	26.685	26.652	26.652	26.652
observation->ObserverProportionsAtAge-2008	37.886	37.882	37.886	37.858	37.858	37.886	37.886	37.886
observation->ObserverProportionsAtAge-2009	20.404	20.478	20.404	20.375	20.375	20.404	20.404	20.404
observation->ObserverProportionsAtAge-2010	27.646	27.656	27.646	27.660	27.660	27.646	27.646	27.646
observation->ObserverProportionsAtAge-2011	25.050	25.101	25.050	25.087	25.087	25.050	25.050	25.050
observation->ObserverProportionsAtAge-2012	27.283	27.252	27.283	26.836	26.836	27.283	27.283	27.283
observation->ObserverProportionsAtAge-2013	25.155	25.124	25.155	27.976	27.976	25.155	25.155	25.155
observation->ObserverProportionsAtAge-2014	49.117	48.937	49.117	35.395	35.395	49.117	49.117	49.117
observation->ObserverProportionsAtAge-2015	34.203	34.231	34.203	28.362	28.362	34.203	34.203	34.203
prior->B0->process[Recruitment].b0	12.610	12.608	12.610	12.659	12.659	12.610	12.610	12.610
prior->Migration_male->selectivity[MaturationSel_male].v{1}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_male->selectivity[MaturationSel_male].v{2}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_male->selectivity[MaturationSel_male].v{3}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_male->selectivity[MaturationSel_male].v{4}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_female->selectivity[MaturationSel_female].v{1}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_female->selectivity[MaturationSel_female].v{2}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_female->selectivity[MaturationSel_female].v{3}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->Migration_female->selectivity[MaturationSel_female].v{4}	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
prior->YCS->process[Recruitment].ycs_values{1958}	-0.984	-0.984	-0.984	-0.982	-0.982	-0.984	-0.984	-0.984
prior->YCS->process[Recruitment].ycs_values{1959}	-0.982	-0.982	-0.982	-0.979	-0.979	-0.982	-0.982	-0.982
prior->YCS->process[Recruitment].ycs_values{1960}	-0.979	-0.979	-0.979	-0.976	-0.976	-0.979	-0.979	-0.979
prior->YCS->process[Recruitment].ycs_values{1961}	-0.975	-0.975	-0.975	-0.971	-0.971	-0.975	-0.975	-0.975
prior->YCS->process[Recruitment].ycs_values{1962}	-0.970	-0.969	-0.970	-0.965	-0.965	-0.970	-0.970	-0.970
prior->YCS->process[Recruitment].ycs_values{1963}	-0.962	-0.961	-0.962	-0.955	-0.955	-0.962	-0.962	-0.962
prior->YCS->process[Recruitment].ycs_values{1964}	-0.950	-0.948	-0.950	-0.941	-0.941	-0.950	-0.950	-0.950
prior->YCS->process[Recruitment].ycs_values{1965}	-0.336	-0.327	-0.336	-0.147	-0.147	-0.336	-0.336	-0.336
prior->YCS->process[Recruitment].ycs_values{1966}	-0.730	-0.728	-0.730	-0.622	-0.622	-0.730	-0.730	-0.730
prior->YCS->process[Recruitment].ycs_values{1967}	-0.927	-0.926	-0.927	-0.867	-0.867	-0.927	-0.927	-0.927
prior->YCS->process[Recruitment].ycs_values{1968}	-0.989	-0.989	-0.989	-0.976	-0.976	-0.989	-0.989	-0.989
prior->YCS->process[Recruitment].ycs_values{1969}	-0.793	-0.793	-0.793	-0.867	-0.867	-0.793	-0.793	-0.793
prior->YCS->process[Recruitment].ycs_values{1970}	-0.306	-0.308	-0.306	-0.445	-0.445	-0.306	-0.306	-0.306
prior->YCS->process[Recruitment].ycs_values{1971}	-0.858	-0.859	-0.858	-0.924	-0.924	-0.858	-0.858	-0.858
prior->YCS->process[Recruitment].ycs_values{1972}	-0.574	-0.574	-0.574	-0.700	-0.700	-0.574	-0.574	-0.574
prior->YCS->process[Recruitment].ycs_values{1973}	0.170	0.168	0.170	-0.041	-0.041	0.170	0.170	0.170
prior->YCS->process[Recruitment].ycs_values{1974}	0.101	0.103	0.101	-0.115	-0.115	0.101	0.101	0.101
prior->YCS->process[Recruitment].ycs_values{1975}	-0.708	-0.709	-0.708	-0.821	-0.821	-0.708	-0.708	-0.708
prior->YCS->process[Recruitment].ycs_values{1976}	0.404	0.399	0.404	0.148	0.148	0.404	0.404	0.404
prior->YCS->process[Recruitment].ycs_values{1977}	0.844	0.845	0.844	0.549	0.549	0.844	0.844	0.844
prior->YCS->process[Recruitment].ycs_values{1978}	0.436	0.436	0.436	0.166	0.166	0.436	0.436	0.436
prior->YCS->process[Recruitment].ycs_values{1979}	-0.937	-0.937	-0.937	-0.860	-0.860	-0.937	-0.937	-0.937
prior->YCS->process[Recruitment].ycs_values{1980}	-0.945	-0.945	-0.945	-0.871	-0.871	-0.945	-0.945	-0.945
prior->YCS->process[Recruitment].ycs_values{1981}	-0.414	-0.414	-0.414	-0.598	-0.598	-0.414	-0.414	-0.414
prior->YCS->process[Recruitment].ycs_values{1982}	1.258	1.257	1.258	0.898	0.898	1.258	1.258	1.258
prior->YCS->process[Recruitment].ycs_values{1983}	-0.741	-0.741	-0.741	-0.859	-0.859	-0.741	-0.741	-0.741
prior->YCS->process[Recruitment].ycs_values{1984}	-0.709	-0.707	-0.709	-0.837	-0.837	-0.709	-0.709	-0.709
prior->YCS->process[Recruitment].ycs_values{1985}	-0.584	-0.585	-0.584	-0.742	-0.742	-0.584	-0.584	-0.584
prior->YCS->process[Recruitment].ycs_values{1986}	-0.989	-0.989	-0.989	-0.962	-0.962	-0.989	-0.989	-0.989
prior->YCS->process[Recruitment].ycs_values{1987}	-0.692	-0.691	-0.692	-0.824	-0.824	-0.692	-0.692	-0.692
prior->YCS->process[Recruitment].ycs_values{1988}	-0.883	-0.883	-0.883	-0.771	-0.771	-0.883	-0.883	-0.883
prior->YCS->process[Recruitment].ycs_values{1989}	1.076	1.074	1.076	0.726	0.726	1.076	1.076	1.076
prior->YCS->process[Recruitment].ycs_values{1990}	-0.987	-0.987	-0.987	-0.982	-0.982	-0.987	-0.987	-0.987
prior->YCS->process[Recruitment].ycs_values{1991}	1.692	1.693	1.692	2.159	2.159	1.692	1.692	1.692
prior->YCS->process[Recruitment].ycs_values{1992}	-0.736	-0.735	-0.736	-0.578	-0.578	-0.736	-0.736	-0.736
prior->YCS->process[Recruitment].ycs_values{1993}	-0.989	-0.989	-0.989	-0.978	-0.978	-0.989	-0.989	-0.989
prior->YCS->process[Recruitment].ycs_values{1994}	-0.700	-0.700	-0.700	-0.819	-0.819	-0.700	-0.700	-0.700
prior->YCS->process[Recruitment].ycs_values{1995}	-0.733	-0.739	-0.733	-0.576	-0.576	-0.733	-0.733	-0.733
prior->YCS->process[Recruitment].ycs_values{1996}	-0.950	-0.948	-0.950	-0.879	-0.879	-0.950	-0.950	-0.950
prior->YCS->process[Recruitment].ycs_values{1997}	-0.790	-0.788	-0.790	-0.888	-0.888	-0.790	-0.790	-0.790
prior->YCS->process[Recruitment].ycs_values{1998}	-0.977	-0.977	-0.977	-0.929	-0.929	-0.977	-0.977	-0.977
prior->YCS->process[Recruitment].ycs_values{1999}	-0.929	-0.927	-0.929	-0.976	-0.976	-0.929	-0.929	-0.929
prior->YCS->process[Recruitment].ycs_values{2000}	-0.986	-0.986	-0.986	-0.951	-0.951	-0.986	-0.986	-0.986
prior->YCS->process[Recruitment].ycs_values{2001}	-0.552	-0.555	-0.552	-0.339	-0.339	-0.552	-0.552	-0.552
prior->YCS->process[Recruitment].ycs_values{2002}	-0.909	-0.907	-0.909	-0.801	-0.801	-0.909	-0.909	-0.909
prior->YCS->process[Recruitment].ycs_values{2003}	-0.985	-0.985	-0.985	-0.983	-0.983	-0.985	-0.985	-0.985
prior->YCS->process[Recruitment].ycs_values{2004}	-0.983	-0.982	-0.983	-0.984	-0.984	-0.983	-0.983	-0.983
prior->YCS->process[Recruitment].ycs_values{2005}	-0.982	-0.982	-0.982	-0.924	-0.924	-0.982	-0.982	-0.982
prior->YCS->process[Recruitment].ycs_values{2006}	0.571	0.571	0.571	1.057	1.057	0.571	0.571	0.571
prior->YCS->process[Recruitment].ycs_values{2007}	-0.636	-0.640	-0.636	-0.369	-0.369	-0.636	-0.636	-0.636
prior->YCS->process[Recruitment].ycs_values{2008}	-0.910	-0.907	-0.910	-0.982	-0.982	-0.910	-0.910	-0.910
prior->YCS->process[Recruitment].ycs_values{2009}	-0.066	-0.080	-0.066	0.419	0.419	-0.066	-0.066	-0.066
prior->YCS->process[Recruitment].ycs_values{2010}	4.782	4.783	4.782	-0.947	-0.947	4.782	4.782	4.782
prior->YCS->process[Recruitment].ycs_values{2011}	-0.526	-0.535	-0.526	-0.067	-0.067	-0.526	-0.526	-0.526
prior->YCS->process[Recruitment].ycs_values{2012}	-0.607	-0.603	-0.607	-0.845	-0.845	-0.607	-0.607	-0.607
prior->M_male_with_avg_prior->process[Instantaneous_Mortality].m{male.nonspawn}	-1.354	-1.362	-1.354	-1.183	-1.183	-1.354	-1.354	-1.354
prior->M_female_with_diff_prior->process[Instantaneous_Mortality].m{female.nonspawn}	0.016	0.017	0.016	0.017	0.017	0.016	0.016	0.016
prior->mature_process_error->observation[TangaroaAcousticMature].process_error	-9.210	-9.210	-9.210	-9.210	-9.210	-9.210	-9.210	-9.210
additional_prior->Penalty-YCS	0.483	0.483	0.483	0.397	0.397	0.483	0.483	0.483
additional_prior->TangaroaMatureq	-0.713	-0.712	-0.713	-0.732	-0.732	-0.713	-0.713	-0.713
jacobian->avg_diff	0.000	0.000	0.000	0.000	0.000	0.000	0.000	0.000
total_negloglike	962.721	962.900	962.721	938.228	938.228	962.721	962.721	962.721

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-006"                                                                  
## [2] "fmm: have converged: t = 1.56689e-006 f = 938.352"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 260 quasi-Newton iterations using 321 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-009"                                                                                 
## [2] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [3] "Successful convergence in optimise"                                                                                      
## [4] "Minimiser achieved convergence after 270 quasi-Newton iterations using 338 objective function evaluations"               
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.98341e-07 f = 973.615"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.84259e-07 f = 973.79"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [2] "Successful convergence in optimise"                                                                                      
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       67"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     2278"
##  [4] "Number of Iterations....: 66"                                   
##  [5] "Number of objective function evaluations             = 89"      
##  [6] "Number of objective gradient evaluations             = 67"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 89"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 67"      
## [11] "Number of Lagrangian Hessian evaluations             = 66"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       67"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     2278"
##  [4] "Number of Iterations....: 66"                                   
##  [5] "Number of objective function evaluations             = 89"      
##  [6] "Number of objective gradient evaluations             = 67"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 89"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 67"      
## [11] "Number of Lagrangian Hessian evaluations             = 66"      
## [12] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)

## [1] "CASAL model warnings"
##                                                      parameter estimate
## 1  relative_abundance[TangaroaAcousticMature].cv_process_error   0.0001
## 2                           migration[toSpawn].rates_female[4]    0.999
## 3                                          recruitment.YCS[13]  0.08025
## 4                                          recruitment.YCS[16]  0.05757
## 5                                          recruitment.YCS[17]  0.06079
## 6                                          recruitment.YCS[19]  0.05057
## 7                                          recruitment.YCS[20]  0.03959
## 8                                          recruitment.YCS[21]  0.04996
## 9                                          recruitment.YCS[24]  0.09402
## 10                                         recruitment.YCS[25]   0.0328
## 11                                         recruitment.YCS[32]   0.0359
##    lower.bound upper.bound
## 1       0.0001           1
## 2        0.001       0.999
## 3        0.001         100
## 4        0.001         100
## 5        0.001         100
## 6        0.001         100
## 7        0.001         100
## 8        0.001         100
## 9        0.001         100
## 10       0.001         100
## 11       0.001         100
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                                                      parameter estimate
## 1  relative_abundance[TangaroaAcousticMature].cv_process_error   0.0001
## 2                           migration[toSpawn].rates_female[4]    0.999
## 3                                          recruitment.YCS[13]  0.08025
## 4                                          recruitment.YCS[16]  0.05757
## 5                                          recruitment.YCS[17]  0.06079
## 6                                          recruitment.YCS[19]  0.05057
## 7                                          recruitment.YCS[20]  0.03959
## 8                                          recruitment.YCS[21]  0.04996
## 9                                          recruitment.YCS[24]  0.09402
## 10                                         recruitment.YCS[25]   0.0328
## 11                                         recruitment.YCS[32]   0.0359
##    lower.bound upper.bound
## 1       0.0001           1
## 2        0.001       0.999
## 3        0.001         100
## 4        0.001         100
## 5        0.001         100
## 6        0.001         100
## 7        0.001         100
## 8        0.001         100
## 9        0.001         100
## 10       0.001         100
## 11       0.001         100
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## $warnings_found
## [1] 5
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_male].v{4}' was within 0.001 of lower bound 0.001"
## 
## $warning_2
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_3
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_4
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others...

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.5771 0.7601"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.465 0.7616"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.496137678991627 0.754222111654299"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.477568420867415 0.766082936063558"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.494542407877019 0.753488756509326"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): 0 0"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): 0 0"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.449867451595697 0.765859852647084"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.475954909278459 0.77245952551618"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.450174071110356 0.76519971244179"